From 8dda32d9a853a6b551df1600c99db94c34dd29b4 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Fri, 22 Sep 2023 17:41:19 +0100
Subject: [PATCH 1/7] To v0.13.0

---
 jnml                                    | 2 +-
 jnml.bat                                | 2 +-
 pom.xml                                 | 6 +++---
 src/main/java/org/neuroml/JNeuroML.java | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/jnml b/jnml
index 5a5ae99..b219451 100755
--- a/jnml
+++ b/jnml
@@ -5,7 +5,7 @@
 #   Type java -X for more info
 export JNML_MAX_MEMORY=400M
 
-export JNML_VERSION=0.12.4
+export JNML_VERSION=0.13.0
 
 
 export CLASSPATH=.:./target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar:$JNML_HOME/target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar
diff --git a/jnml.bat b/jnml.bat
index 2702580..c3b26ef 100644
--- a/jnml.bat
+++ b/jnml.bat
@@ -1,6 +1,6 @@
 @echo off
 
-set JNML_VERSION=0.12.4
+set JNML_VERSION=0.13.0
 
 set CLASSPATH=target\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar;%JNML_HOME%\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar
 
diff --git a/pom.xml b/pom.xml
index 889ee05..4427225 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>org.neuroml</groupId>
     <artifactId>jNeuroML</artifactId>
-    <version>0.12.4</version>
+    <version>0.13.0</version>
     <packaging>jar</packaging>
 
     <name>jNeuroML</name>
@@ -24,12 +24,12 @@
         <dependency>
             <groupId>org.neuroml1.model</groupId>
             <artifactId>org.neuroml1.model</artifactId>
-            <version>1.9.1</version>
+            <version>1.10.0</version>
         </dependency>
         <dependency>
             <groupId>org.neuroml.import</groupId>
             <artifactId>org.neuroml.import</artifactId>
-            <version>1.9.1</version>
+            <version>1.10.0</version>
         </dependency>
 
         <!-- Dependencies to force use of log4j 2.17.1 -->
diff --git a/src/main/java/org/neuroml/JNeuroML.java b/src/main/java/org/neuroml/JNeuroML.java
index d08e543..38c19e8 100644
--- a/src/main/java/org/neuroml/JNeuroML.java
+++ b/src/main/java/org/neuroml/JNeuroML.java
@@ -60,7 +60,7 @@ public class JNeuroML
 
     public static final String JNML_SCRIPT = "jnml";
 
-    public static final String JNML_VERSION = "0.12.4";
+    public static final String JNML_VERSION = "0.13.0";
 
     public static final String HELP_FLAG = "-help";
     public static final String HELP_FLAG_SHORT = "-h";

From 9119be74f4cdb187703f36833ec41548a4fba095 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Wed, 1 May 2024 11:56:13 +0100
Subject: [PATCH 2/7] Test on java 21

---
 .github/workflows/ci.yml   | 13 +++++++++----
 .github/workflows/docs.yml | 21 +++++++++++----------
 pom.xml                    |  4 ++--
 3 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9d134e6..6cc3357 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,14 +16,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17', '19']
-        runs-on: [ubuntu-latest, macos-latest, windows-2019 ]
+        java: [ '8', '11', '16', '17', '19', '21' ]
+        runs-on: [ubuntu-latest, macos-12, windows-2019] # Note macos-12, not latest/14, due to hdf5 install issue
+        exclude:
+          - runs-on: macos-latest
+            java: "8"
+          - runs-on: macos-latest
+            java: "16"
 
     name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.Java }}
         distribution: 'adopt'
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index fdf1f45..01a06d7 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -13,17 +13,18 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: nelonoel/branch-name@v1.0.1
 
     - name: Set up JDK 11
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v4
       with:
         java-version: 11
         java-package: jdk
+        distribution: 'temurin'
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
@@ -33,49 +34,49 @@ jobs:
         pip install ghp-import
 
     - name: Checkout NeuroML2
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/NeuroML2
         ref: development
         path: NeuroML2
 
     - name: Checkout org.lemsml
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: LEMS/jLEMS
         ref: development
         path: jLEMS
 
     - name: Checkout org.neuroml.model.injectingplugin
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.model.injectingplugin
         ref: development
         path: org.neuroml.model.injectingplugin
 
     - name: Checkout org.neuroml1.model
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml1.model
         ref: development
         path: org.neuroml1.model
 
     - name: Checkout org.neuroml.model
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.model
         ref: development
         path: org.neuroml.model
 
     - name: Checkout org.neuroml.export
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.export
         ref: development
         path: org.neuroml.export
 
     - name: Checkout org.neuroml.import
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: NeuroML/org.neuroml.import
         ref: development
diff --git a/pom.xml b/pom.xml
index 4427225..5608e69 100644
--- a/pom.xml
+++ b/pom.xml
@@ -95,8 +95,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.0</version>
                 <configuration>
-                    <source>1.7</source>
-                    <target>1.7</target>
+                    <source>1.8</source>
+                    <target>1.8</target>
                 </configuration>
             </plugin>
 

From 9a8d655217caa312e29e75b869ed64d311499ca6 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Tue, 11 Jun 2024 12:02:29 +0100
Subject: [PATCH 3/7] To v1.10.1

---
 jnml                                    | 2 +-
 jnml.bat                                | 2 +-
 pom.xml                                 | 6 +++---
 src/main/java/org/neuroml/JNeuroML.java | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/jnml b/jnml
index b219451..bc75266 100755
--- a/jnml
+++ b/jnml
@@ -5,7 +5,7 @@
 #   Type java -X for more info
 export JNML_MAX_MEMORY=400M
 
-export JNML_VERSION=0.13.0
+export JNML_VERSION=0.13.1
 
 
 export CLASSPATH=.:./target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar:$JNML_HOME/target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar
diff --git a/jnml.bat b/jnml.bat
index c3b26ef..addf823 100644
--- a/jnml.bat
+++ b/jnml.bat
@@ -1,6 +1,6 @@
 @echo off
 
-set JNML_VERSION=0.13.0
+set JNML_VERSION=0.13.1
 
 set CLASSPATH=target\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar;%JNML_HOME%\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar
 
diff --git a/pom.xml b/pom.xml
index 5608e69..16e96fd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>org.neuroml</groupId>
     <artifactId>jNeuroML</artifactId>
-    <version>0.13.0</version>
+    <version>0.13.1</version>
     <packaging>jar</packaging>
 
     <name>jNeuroML</name>
@@ -24,12 +24,12 @@
         <dependency>
             <groupId>org.neuroml1.model</groupId>
             <artifactId>org.neuroml1.model</artifactId>
-            <version>1.10.0</version>
+            <version>1.10.1</version>
         </dependency>
         <dependency>
             <groupId>org.neuroml.import</groupId>
             <artifactId>org.neuroml.import</artifactId>
-            <version>1.10.0</version>
+            <version>1.10.1</version>
         </dependency>
 
         <!-- Dependencies to force use of log4j 2.17.1 -->
diff --git a/src/main/java/org/neuroml/JNeuroML.java b/src/main/java/org/neuroml/JNeuroML.java
index 38c19e8..87dbde6 100644
--- a/src/main/java/org/neuroml/JNeuroML.java
+++ b/src/main/java/org/neuroml/JNeuroML.java
@@ -60,7 +60,7 @@ public class JNeuroML
 
     public static final String JNML_SCRIPT = "jnml";
 
-    public static final String JNML_VERSION = "0.13.0";
+    public static final String JNML_VERSION = "0.13.1";
 
     public static final String HELP_FLAG = "-help";
     public static final String HELP_FLAG_SHORT = "-h";

From fe28397c99c967e0501fd6be175e77769a7e097d Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Tue, 11 Jun 2024 12:22:30 +0100
Subject: [PATCH 4/7] Bump year in docs

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 16e96fd..1671717 100644
--- a/pom.xml
+++ b/pom.xml
@@ -59,7 +59,7 @@
                             &lt;br /&gt;
                             &lt;br /&gt;
                     </top>
-                    <bottom>Copyright NeuroML Contributors 2023</bottom>
+                    <bottom>Copyright NeuroML Contributors 2024</bottom>
                 </configuration>
             </plugin>
             <plugin>

From 7538a96113044141f5dd4469dd9b1542ea142b17 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 18 Jun 2024 09:15:55 +0100
Subject: [PATCH 5/7] To v0.13.2

---
 jnml                                    | 2 +-
 jnml.bat                                | 2 +-
 pom.xml                                 | 2 +-
 src/main/java/org/neuroml/JNeuroML.java | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/jnml b/jnml
index bc75266..8dc4a8b 100755
--- a/jnml
+++ b/jnml
@@ -5,7 +5,7 @@
 #   Type java -X for more info
 export JNML_MAX_MEMORY=400M
 
-export JNML_VERSION=0.13.1
+export JNML_VERSION=0.13.2
 
 
 export CLASSPATH=.:./target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar:$JNML_HOME/target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar
diff --git a/jnml.bat b/jnml.bat
index addf823..5428cf5 100644
--- a/jnml.bat
+++ b/jnml.bat
@@ -1,6 +1,6 @@
 @echo off
 
-set JNML_VERSION=0.13.1
+set JNML_VERSION=0.13.2
 
 set CLASSPATH=target\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar;%JNML_HOME%\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar
 
diff --git a/pom.xml b/pom.xml
index 1671717..adea2b4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>org.neuroml</groupId>
     <artifactId>jNeuroML</artifactId>
-    <version>0.13.1</version>
+    <version>0.13.2</version>
     <packaging>jar</packaging>
 
     <name>jNeuroML</name>
diff --git a/src/main/java/org/neuroml/JNeuroML.java b/src/main/java/org/neuroml/JNeuroML.java
index 87dbde6..512d2a9 100644
--- a/src/main/java/org/neuroml/JNeuroML.java
+++ b/src/main/java/org/neuroml/JNeuroML.java
@@ -60,7 +60,7 @@ public class JNeuroML
 
     public static final String JNML_SCRIPT = "jnml";
 
-    public static final String JNML_VERSION = "0.13.1";
+    public static final String JNML_VERSION = "0.13.2";
 
     public static final String HELP_FLAG = "-help";
     public static final String HELP_FLAG_SHORT = "-h";

From 4f91af86dd1d7c6344a2492ca1fa346f44ff53a6 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Mon, 19 Aug 2024 12:27:57 +0100
Subject: [PATCH 6/7] To v0.13.3

---
 jnml                                    | 2 +-
 jnml.bat                                | 2 +-
 pom.xml                                 | 2 +-
 src/main/java/org/neuroml/JNeuroML.java | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/jnml b/jnml
index 8dc4a8b..3156f11 100755
--- a/jnml
+++ b/jnml
@@ -5,7 +5,7 @@
 #   Type java -X for more info
 export JNML_MAX_MEMORY=400M
 
-export JNML_VERSION=0.13.2
+export JNML_VERSION=0.13.3
 
 
 export CLASSPATH=.:./target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar:$JNML_HOME/target/jNeuroML-$JNML_VERSION-jar-with-dependencies.jar
diff --git a/jnml.bat b/jnml.bat
index 5428cf5..f943f08 100644
--- a/jnml.bat
+++ b/jnml.bat
@@ -1,6 +1,6 @@
 @echo off
 
-set JNML_VERSION=0.13.2
+set JNML_VERSION=0.13.3
 
 set CLASSPATH=target\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar;%JNML_HOME%\jNeuroML-%JNML_VERSION%-jar-with-dependencies.jar
 
diff --git a/pom.xml b/pom.xml
index adea2b4..946fb16 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>org.neuroml</groupId>
     <artifactId>jNeuroML</artifactId>
-    <version>0.13.2</version>
+    <version>0.13.3</version>
     <packaging>jar</packaging>
 
     <name>jNeuroML</name>
diff --git a/src/main/java/org/neuroml/JNeuroML.java b/src/main/java/org/neuroml/JNeuroML.java
index 512d2a9..e081c15 100644
--- a/src/main/java/org/neuroml/JNeuroML.java
+++ b/src/main/java/org/neuroml/JNeuroML.java
@@ -60,7 +60,7 @@ public class JNeuroML
 
     public static final String JNML_SCRIPT = "jnml";
 
-    public static final String JNML_VERSION = "0.13.2";
+    public static final String JNML_VERSION = "0.13.3";
 
     public static final String HELP_FLAG = "-help";
     public static final String HELP_FLAG_SHORT = "-h";

From 0c2f611cfb9d220ac90af19d551ea1e33d2a259b Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Tue, 20 Aug 2024 14:56:35 +0100
Subject: [PATCH 7/7] Move to temurin

Fixes #101
---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6cc3357..c4f304e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
       uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.Java }}
-        distribution: 'adopt'
+        distribution: 'temurin'
 
     - name: Install using getNeuroML.py (non Win)
       env: